Rendering multiple layers, missing background
Your model is receiving purple colour from the world material settings. There are two ways of dealing with this.

Compositor Method - If you simply want to add a background behind your render, you could change the world colour to white or anything else, and in the Compositor, plug in the render result into the bottom input of an Alpha Over node, and simply set the colour of your background in the other input setting. In your case, this step would come after your freestyle composite so you'll be adding a second Alpha Over.



Shader Method - If you want your actual scene background to have a different colour from what's being cast onto the objects, then in your world material, add a second Background shader. Connect this into a Mix shader along with the original Background shader. Then add a Light Path node and connect its &quot;Is Camera Ray&quot; output into the factor of the Mix node. And voila, now basically the colour on the top input of the mix is the one that the objects will receive but is not visible to us, and the second input is the one that we see but won't affect the scene.


Hope that makes sense! :)